Re: [Obo-human-phenotype] has extra parts of type

[George G. <gg...@ca...>]

On 11 Dec 2010, at 10:17, Robinson, Peter wrote:

> Hi,
>
> for the definitions of metabolic abnormalities in which the  
> concentration of a substance in the blood or urine is increased, I  
> would prefer to use
>
> PATO:0001162 ! increased concentration
>
> rather than PATO:0002002 ! has extra parts of type.
>
> For instance:
>
>
> [Term]
> id: HP:0002903 ! Aminoaciduria
> intersection_of: PATO:0002002 ! has extra parts of type
> intersection_of: inheres_in FMA:12274 ! Urine
> intersection_of: towards CHEBI:33709 ! amino acids
>
>
> I think this came about because we said that normally you should not  
> be able to measure any amino acids in the urine. However, increased  
> concentration is  correct in any case, and I think that it will be  
> easier to make inferences if we agree just to use this term. After  
> all, presumably there are a few molecules of everything anywhere if  
> you look hard enough. The only other thing to consider is if we  
> should add "abnormal" as a qualifier to all these terms.
>
> What do you think?


I have been using increased concentration in similar cases - I think  
it reflects better what we are trying to represent.

George

>
> -Peter
>
>
>
> PD Dr. med. Peter N. Robinson, MSc.
> Institut für Medizinische Genetik
> Charité - Universitätsmedizin Berlin
> Augustenburger Platz 1
> 13353 Berlin
> Germany
> +4930 450566042
> pet...@ch...
> http://compbio.charite.de
> http://www.human-phenotype-ontology.org
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---------------------------------------------------
Dr. G.V.Gkoutos

University of Cambridge
Department of Genetics
Downing Site, Downing Street
Cambridge, CB2 3EH

Tel: +44 [0] 01223 766336

email: gg...@ca...
url: http://www.gen.cam.ac.uk

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